Silencing genes to cure diseases: an in-depth look at siRNA

siRNA

Discovered in the late 1990s, Small interfering RNA (siRNA) is a class of double-stranded RNA molecules, involved in the RNA interference (RNAi) pathway, where it mediates the silencing of specific genes.

The use of siRNA in research and medicine has evolved significantly since its discovery, with ongoing development focused on overcoming challenges such as delivering siRNA molecules into cells efficiently and specifically targeting disease-causing genes while minimizing off-target effects. The success of siRNA technology in the lab has led to the development of siRNA-based therapeutics, which are now beginning to be approved for clinical use in treating diseases with genetic components​​.

Recent developments, such as the approval of new siRNA-based drugs and advancements in delivery mechanisms are signaling a promising era for gene-targeted therapies. The siRNA technology sector is gaining momentum as major biotech players have recently increased their focus on siRNA.

Table of contents

    How does siRNA work?

    SiRNA plays a crucial role in gene silencing by following a multi-step process called RNA interference (RNAi). siRNA is created by cutting long double-stranded RNA molecules into shorter pieces that are then integrated into an RNA-induced silencing complex (RISC). Then, siRNA helps identify and bind to a matching messenger mRNA molecule, which is a copy of the gene that needs to be silenced. Once bound to the mRNA, the RISC, guided by siRNA, cuts the mRNA, thereby destroying it. With the mRNA degraded, it can no longer be used to make protein, leading to the silencing of the gene activity from which the mRNA was transcribed.

    siRNA Figure

    Figure of the siRNA originally published by Biopharma PEG.

    SiRNAs are distinct from other RNA types, such as microRNA (miRNA) and Piwi-interacting RNA (piRNA), in their source, structure, and function. While miRNAs and piRNAs also participate in gene silencing, they have broader specificity and different mechanisms of action. miRNAs generally regulate gene expression by repressing translation and can have multiple target mRNAs, whereas siRNAs are more specific, targeting and cleaving mRNA sequences with near-perfect complementarity.

    SiRNA is being explored for therapeutic applications, especially in targeting viral infections. siRNAs can be designed to specifically target and silence genes crucial for the survival and replication of viruses, such as those involved in the life cycle of human immunodeficiency virus HIV, hepatitis B, and respiratory syncytial virus (RSV). However, the development and clinical application of siRNA-based therapies face challenges, including ensuring the stability and delivery of siRNA molecules, avoiding off-target effects, and overcoming immune responses.

    Where do we stand in siRNA therapeutics?

    SiRNA is a very dynamic field involving biotech leaders such as Amgen and AstraZeneca, and specialized companies often collaborating to bring therapeutics to the market. 

    On the side of AstraZeneca, its candidate eplontersen developed in collaboration with Ionis Pharmaceuticals was recently greenlit by the U.S. Food and Drug Administration (FDA). Sold under the brand name Wainua, it is aimed at treating hereditary transthyretin-mediated amyloidosis (hATTR), condition where the protein transthyretin (TTR) becomes misfolded and accumulates as amyloid fibrils in various body tissues, including nerves, heart, and gastrointestinal system.

    The approval of Eplontersen was based on positive results from the phase 3 NEURO-TTRansform study, which demonstrated the drug’s consistent and sustained benefit in halting disease progression and improving both neuropathy impairment and quality of life for patients. Eplontersen is significant for being self-administrable via an auto-injector, offering convenience and a better quality of life for patients with this condition.

    Alnylam Pharmaceuticals has been a leader in this field, with ONPATTRO (patisiran) being the first siRNA drugs approved by the FDA for the treatment of polyneuropathy caused by hATTR. Following this, other siRNA therapeutics like GIVLAARI (givosiran) for acute hepatic porphyria, and Oxlumo (lumasiran) for primary hyperoxaluria type 1 have also been approved, showcasing the growing versatility and potential of siRNA-based treatments​​.

    Advancements in siRNA therapeutics, particularly with drugs like Inclisiran, represent significant progress in the management of conditions like hypercholesterolemia. Inclisiran, developed by Novartis, is the first siRNA drug approved for reducing low-density lipoprotein cholesterol (LDL-C) levels in patients with hypercholesterolemia or mixed dyslipidemia, as well as in those with atherosclerotic cardiovascular disease (ASCVD) or heterozygous familial hypercholesterolemia (HeFH) who require further LDL-C reduction.

    Inclisiran targets PCSK9, a protein that regulates the number of LDL receptors on the liver surface, influencing LDL-C levels in the blood. By reducing PCSK9 production, Inclisiran increases the presence of LDL receptors, thereby enhancing the clearance of LDL-C from the bloodstream. A significant advantage of Inclisiran is its dosing frequency, which is considerably less frequent than that of monoclonal antibodies, the other main class of PCSK9 inhibitors. Inclisiran’s extended duration of action allows for dosing just twice a year, which could improve patient compliance and reduce treatment burdens.

    What is in the siRNA pipelines?

    Alnylam continues to push its siRNA pipeline of investigational RNAi therapeutics targeting various diseases. Notable among these is Fitusiran, an investigational siRNA therapeutic for the treatment of hemophilia A and B, which is being developed in collaboration with Sanofi and is expected to see a New Drug Application filed in 2024. Alnylam is also developing ALN-BCAT, targeting β-catenin for hepatocellular carcinoma, with a phase 1 study initiation planned in early 2024. The company is exploring treatments for other conditions too, including cardiovascular diseases with vutrisiran, and metabolic and neurodegenerative disorders with ALN-APP for Alzheimer’s disease​​.

    The biotech giant Amgen is also developing a siRNA candidate in collaboration with Arrowhead Pharmaceuticals. Olpasiran, aimed at treating atherosclerosis by targeting apolipoprotein(a), a component of lipoprotein(a), (Lp(a)) is currently in phase 3 clinical trials. Elevated Lp(a) levels are associated with an increased risk of cardiovascular events. Olpasiran has shown significant promise in clinical trials, particularly in the phase 2 OCEAN(a)-DOSE study, where it demonstrated a substantial reduction in Lp(a) levels in patients with established atherosclerotic cardiovascular disease (ASCVD) and elevated Lp(a).

    Novo Nordisk joined the siRNA race in 2021 with the acquisition of Dicerna, a company that has been at the forefront of developing RNAi technologies. The company’s work primarily revolves around its proprietary GalXC and GalXC-Plus RNAi technologies. These platforms are designed to selectively silence genes that contribute to diseases. The acquisition of Dicerna by Novo Nordisk represents a strategic move to enhance the development and commercialization of GalXC RNAi therapies, aiming to bring novel treatments to patients with serious chronic diseases. 

    Earlier this year, another key player in the industry, Boehringer Ingelheim entered a collaboration worth over $2 billion with Suzhou Ribo Life Science and Ribocure Pharmaceuticals to develop siRNA therapeutics for liver diseases like NASH/MASH. The partnership leverages Ribo’s RIBO-GalSTAR platform to create treatments that target disease-causing genes in hepatocytes by silencing their mRNA.

    Other notable candidates include Silence Therapeutics’zerlasiran (SLN360), currently in phase 2, developed for cardiovascular disease, specifically targeting Lp(a) to lower the risk of heart-related conditions such as heart attacks and strokes. The company is also developing divesiran (SLN124) focused on hematological diseases targeting the TMPRSS6 gene. By silencing this gene, the therapy aims to increase hepcidin production in the liver, which can help manage iron levels in the body and address conditions like polycythemia vera (PV). This candidate has advanced to clinical studies and has received Fast Track and orphan drug designations from the FDA.

    The hype around SiRNA is justified as it is a very versatile technology with new candidates being developed and approved therapeutics being explored for new applications and targets.

    SiRNA’s future: Overcoming challenges and improving delivery

    The challenges facing siRNA therapeutics are multifaceted, spanning biological, chemical, and technical aspects. One primary concern is the non-specific uptake of siRNA by non-target cells, including immune and non-cancerous cells, which can lead to unintended gene silencing and toxicity. This occurs because siRNA molecules, once administered into the body, can be taken up by various cells, not just the ones they are meant to target. For instance, if siRNA designed to silence a gene in cancer cells is also taken up by immune cells, it might inadvertently suppress genes critical for the immune system’s functioning, leading to immunosuppression. To mitigate these issues, advancements such as chemical modifications of siRNA for stability and reduced protein binding, and the use of tissue-specific targeting ligands are being explored​.

    Intracellularly, siRNA technology faces barriers like membrane permeability and endosomal escape. The hydrophilic and negatively charged nature of siRNA complicates its delivery across the hydrophobic lipid bilayer of cell membranes. Once inside the cell, siRNA can become entrapped in endosomes, leading to degradation or sequestration, diminishing its therapeutic efficacy. Strategies to overcome these barriers include pH-sensitive liposomes, cell-penetrating peptides, endosomal disruptors, and various nanoparticles designed to facilitate endosomal escape and ensure the release of siRNA into the cytoplasm​​.

    The effective design of siRNA sequences to target specific mRNA sites without off-target effects, enhancing biological stability in the bloodstream, and optimizing delivery systems for improved cell uptake and pharmacokinetics are crucial. The complex nature and large molecular weight of siRNA necessitate sophisticated delivery systems to navigate the biological environment and reach the target cells effectively​.

    The future of siRNA therapy is geared towards enhancing its delivery, particularly through nanoparticle systems like lipid-based nanoparticles (LNPs). These advancements aim to improve siRNA’s stability, targeting, and cellular uptake, broadening its therapeutic applications. Key areas of focus include targeting challenging diseases and refining nanoparticle designs to minimize off-target effects and enhance tissue-specific delivery. This evolution in siRNA delivery technologies holds the promise of transforming treatment options for a variety of diseases, potentially marking a new era in therapeutic interventions.

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